add stix query script

mchowdh200 · Jul 7, 2022 · e6c24f6 · e6c24f6
1 parent 8b98282
commit e6c24f6
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diff --git a/scripts/construct_queries.py b/scripts/construct_queries.py
@@ -1,6 +1,7 @@
 """
 Construct the -l and -r region strings from the vcf
 regions/confidence intervals separated by a tab.
+Includes SVTYPE of query in final column.
 """
 import sys
 import pysam

diff --git a/stix_1kg_dels.smk b/stix_1kg_dels.smk
@@ -11,8 +11,26 @@ rule ConstructQueries:
     """
     input: config.vcf
     output: f'{config.outdir}/queries.txt'
-    threads: workflow.cores
+    threads: 1
     conda: 'envs/pysam.yaml'
     shell:
         'python scripts/construct_queries.py {input} DEL > {output}'
 
+
+rule StixQuery:
+    """
+    TODO run on just a handfull of regions before kicking off the full job
+    Parse the queries file with gargs to run stix queries in parallel
+    """
+    input: rules.ConstructQueries.output
+    output: f'{config.outdir}/query_results.txt'
+    threads: workflow.cores
+    shell:
+        f"""
+        bash scripts/stix_query.sh \\
+        -q {{input}} \\
+        -i {config.stix_index} \\
+        -d {config.stix_db} \\
+        -t {{threads}} \\
+        > {{output}}
+        """